Is it more a yawing type instability sensation, or all axes?
Sounds like a slight lateral instabilty caused by higher yaw moments of the longer fuselage - the longer distance from the datum in the -300 compared to the -200 is going to amplify the apparent degree of yaw for the same amount of instabilty. A simple diagramme would help me here, but I think you get what I mean - the distance disturbed from the centreline is going to be more apparent in a longer fuselage than in the shorter fuselage -200, for the same given parameters.
I do not fly the 757 (WORSE LUCK!), but I assume the fin and wing dimensions are the same for both types?